6YMX: CIII2/CIV respiratory supercomplex from Saccharomyces cerevisiae

PDB ID: 6YMXDownload
MMDB ID: 192203
PDB Deposition Date: 2020/4/10
Updated in MMDB: 2025/12
Experimental Method:
electron microscopy
Resolution: 3.17  Å
Source Organism:
Similar Structures:
Biological Unit for 6YMX: 32-meric; determined by author and by software (PISA)
Molecular Components in 6YMX
Label Count Molecule
Proteins (32 molecules)
1
Cytochrome C Oxidase Subunit 1
(Gene symbol: COX1)
Molecule annotation
1
Cytochrome C Oxidase Subunit 2
(Gene symbol: COX2)
Molecule annotation
1
Cytochrome C Oxidase Subunit 3
(Gene symbol: COX3)
Molecule annotation
1
Cytochrome C Oxidase Subunit 4, Mitochondrial
(Gene symbol: COX4)
Molecule annotation
1
Cytochrome C Oxidase Subunit 5A, Mitochondrial
(Gene symbol: COX5A)
Molecule annotation
1
Cytochrome C Oxidase Subunit 6, Mitochondrial
(Gene symbol: COX6)
Molecule annotation
1
Cytochrome C Oxidase Subunit 7, Mitochondrial
(Gene symbol: COX7)
Molecule annotation
1
Cytochrome C Oxidase Subunit 8, Mitochondrial
(Gene symbol: COX8)
Molecule annotation
1
Cytochrome C Oxidase Subunit 9, Mitochondrial
(Gene symbol: COX9)
Molecule annotation
1
Cytochrome C Oxidase Subunit 12, Mitochondrial
(Gene symbol: COX12)
Molecule annotation
1
Cytochrome C Oxidase Subunit 13, Mitochondrial
(Gene symbol: COX13)
Molecule annotation
1
Cytochrome C Oxidase Subunit 26, Mitochondrial
(Gene symbol: COX26)
Molecule annotation
2
Cytochrome B-c1 Complex Subunit 1, Mitochondrial
(Gene symbol: COR1)
Molecule annotation
2
Cytochrome B-c1 Complex Subunit 2, Mitochondrial
(Gene symbol: QCR2)
Molecule annotation
2
Cytochrome B
(Gene symbol: COB)
Molecule annotation
2
Cytochrome C1, Heme Protein, Mitochondrial
(Gene symbol: CYT1)
Molecule annotation
2
Cytochrome B-c1 Complex Subunit Rieske, Mitochondrial
(Gene symbol: RIP1)
Molecule annotation
1
Cytochrome B-c1 Complex Subunit 6, Mitochondrial
(Gene symbol: QCR6)
Molecule annotation
2
Cytochrome B-c1 Complex Subunit 7, Mitochondrial
(Gene symbol: QCR7)
Molecule annotation
2
Cytochrome B-c1 Complex Subunit 8, Mitochondrial
(Gene symbol: QCR8)
Molecule annotation
1
Cytochrome B-c1 Complex Subunit 9, Mitochondrial
(Gene symbol: QCR9)
Molecule annotation
1
Cytochrome B-c1 Complex Subunit 6, Mitochondrial
(Gene symbol: QCR6)
Molecule annotation
1
Cytochrome B-c1 Complex Subunit 9, Mitochondrial
(Gene symbol: QCR9)
Molecule annotation
1
Cytochrome B-c1 Complex Subunit 10, Mitochondrial
(Gene symbol: QCR10)
Molecule annotation
1
Cytochrome B-c1 Complex Subunit 10, Mitochondrial
(Gene symbol: QCR10)
Molecule annotation
Chemicals and Non-standard biopolymers (38 molecules)
1
1
COPPER (II) IONCOPPER (II) ION
2
2
HEME-AHEME-A
3
7
PHOSPHATIDYLETHANOLAMINEPHOSPHATIDYLETHANOLAMINE
4
2
(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate(2R,5S,11R,14R)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate
5
1
DINUCLEAR COPPER IONDINUCLEAR COPPER ION
6
5
1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE
7
1
ZINC IONZINC ION
8
2
(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate(1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate
9
6
PROTOPORPHYRIN IX CONTAINING FEPROTOPORPHYRIN IX CONTAINING FE
10
2
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
11
1
(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate(5S,11R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate
12
2
5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL
13
2
(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate(1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate
14
2
(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate(1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate
15
2
FE2/S2 (INORGANIC) CLUSTERFE2/S2 (INORGANIC) CLUSTER
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303